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As the heart of the Pirates' operations on Zebes, the Zebesian Command Center was under heavy guard. Cannons and Rinkas fired around this room and in previous rooms to ward off intruders, and Zebetites holding together walls in the room served as impediments to intruders who survived the lava filling the bottom of the chamber.
Samus Aran first confronted and defeated Mother Brain in this room, but was forced to evacuate as the base began to self-destruct. In Zero Mission, returning to the destroyed Command Center revealed that it has since been flooded by Beta Acid, a green substance that was corrosive enough to harm Samus even with her new Gravity Suit active.

Some time after the Command Center's destruction, the Pirates rebuilt the Command Center in a new location, deeper below Zebes. Samus would later revisit the original when she returned to Zebes in search of the Metroid hatchling, only to find it empty and desolate. However, after descending to Brinstar and returning, Samus found that the Space Pirates were indeed still active on the planet, and had been alerted to her presence.

Samus ultimately discovered the rebuilt Command Center's location, and fought Mother Brain once more. As before, the room was filled with lava, but this particularly potent variety was capable of harming Samus even in the Gravity Suit. When Samus seemingly destroyed Mother Brain, her Control Capsule exploded and the supporting pipes collapsed, dropping the AI to the ground. However, the fight was far from over, as Mother Brain attached itself to a large, powerful mechanical body and nearly killed Samus. But before she could strike the finishing blow, the baby appeared and siphoned Mother Brain's energy, transferring it to Samus. Mother Brain revived again, however, and destroyed the baby over Samus. Imbued fwith the energy the hatchling siphoned from her enemy, Samus harnessed the power of the Hyper Beam to kill Mother Brain once and for all. This caused another countdown to be triggered, this time to destroy the entire planet of Zebes. In the process, the Command Center's rear wall exploded, allowing Samus to escape.